eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2014 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.taxeditor.editor.molecular;
  11
  12
  13 import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
  14 import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
  15 import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
  16 import info.bioinfweb.libralign.AlignmentArea;
  17 import info.bioinfweb.libralign.AlignmentContentArea;
  18 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
  19 import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
  20 import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
  21 import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
  22 import info.bioinfweb.libralign.pherogram.PherogramProvider;
  23 import info.bioinfweb.libralign.pherogram.ReverseComplementPherogramProvider;
  24 import info.bioinfweb.libralign.sequenceprovider.SequenceDataProvider;
  25 import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
  26 import info.bioinfweb.libralign.sequenceprovider.implementations.PackedSequenceDataProvider;
  27 import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
  28 import info.bioinfweb.libralign.sequenceprovider.tokenset.TokenSet;
  29
  30 import java.io.File;
  31
  32 import org.biojava.bio.chromatogram.ChromatogramFactory;
  33 import org.biojava3.core.sequence.DNASequence;
  34 import org.biojava3.core.sequence.compound.DNACompoundSet;
  35 import org.biojava3.core.sequence.compound.NucleotideCompound;
  36 import org.eclipse.core.runtime.IProgressMonitor;
  37 import org.eclipse.swt.SWT;
  38 import org.eclipse.swt.widgets.Composite;
  39 import org.eclipse.ui.IEditorInput;
  40 import org.eclipse.ui.IEditorSite;
  41 import org.eclipse.ui.PartInitException;
  42 import org.eclipse.ui.part.EditorPart;
  43
  44
  45
  46 /**
  47  * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
  48  * a consensus sequence.
  49  * <p>
  50  * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
  51  *
  52  * @author Ben Stöver
  53  * @author pplitzner
  54  * @date 04.08.2014
  55  */
  56 public class AlignmentEditor extends EditorPart {
  57     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
  58
  59     private AlignmentArea alignmentArea;
  60
  61
  62         private AlignmentArea createAlignmentArea() {
  63                 try {
  64                         AlignmentArea result = new AlignmentArea();
  65                         AlignmentContentArea contentArea = result.getContentArea();
  66
  67                         TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(new DNACompoundSet(), true);
  68                         SequenceDataProvider<NucleotideCompound> provider = new PackedSequenceDataProvider<NucleotideCompound>(tokenSet);
  69
  70                         // Add index area:
  71                         contentArea.getDataAreas().getTopAreas().add(new SequenceIndexArea(contentArea));
  72
  73
  74                         // First test sequence with pherogram:
  75                         provider.addSequence("Read 1");
  76                         int id = provider.sequenceIDByName("Read 1");
  77                         BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
  78                         new File("D:/Users/BenStoever/Documents/Studium/Projekte/Promotion/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1")));
  79                         //new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1")));
  80
  81                         // Copy base call sequence into alignment:
  82                         for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
  83                                 provider.insertTokenAt(id, i, tokenSet.tokenByKeyChar(pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));
  84                         }
  85
  86                         // Add data area:
  87                         PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
  88                         result.getContentArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
  89
  90
  91                         // Second test sequence with pherogram:
  92                         provider.addSequence("Read 2");
  93                         id = provider.sequenceIDByName("Read 2");
  94                         pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
  95                         new File("D:/Users/BenStoever/Documents/Studium/Projekte/Promotion/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1")));
  96                         //new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1")));
  97                         // Copy base call sequence into alignment:
  98                         for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
  99                                 provider.insertTokenAt(id, i, tokenSet.tokenByKeyChar(pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));
 100                         }
 101
 102                         // Add data area:
 103                         pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
 104                         result.getContentArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
 105
 106
 107                         contentArea.setSequenceProvider(provider, false);
 108
 109                         return result;
 110                 }
 111                 catch (Exception e) {
 112                         throw new RuntimeException(e);
 113                 }
 114         }
 115
 116
 117     /* (non-Javadoc)
 118      * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
 119      */
 120     @Override
 121     public void createPartControl(Composite parent) {
 122         alignmentArea = createAlignmentArea();
 123                 Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);
 124                 //getSite().setSelectionProvider(provider)
 125     }
 126
 127
 128     /* (non-Javadoc)
 129      * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
 130      */
 131     @Override
 132     public void doSave(IProgressMonitor monitor) {
 133         // TODO Auto-generated method stub
 134
 135     }
 136
 137
 138     /* (non-Javadoc)
 139      * @see org.eclipse.ui.part.EditorPart#doSaveAs()
 140      */
 141     @Override
 142     public void doSaveAs() {
 143         // TODO Auto-generated method stub
 144
 145     }
 146
 147
 148     /* (non-Javadoc)
 149      * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
 150      */
 151     @Override
 152     public void init(IEditorSite site, IEditorInput input) throws PartInitException {
 153         setSite(site);
 154         setInput(input);
 155     }
 156
 157
 158     /* (non-Javadoc)
 159      * @see org.eclipse.ui.part.EditorPart#isDirty()
 160      */
 161     @Override
 162     public boolean isDirty() {
 163         // TODO Auto-generated method stub
 164         return false;
 165     }
 166
 167
 168     /* (non-Javadoc)
 169      * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
 170      */
 171     @Override
 172     public boolean isSaveAsAllowed() {
 173         // TODO Auto-generated method stub
 174         return false;
 175     }
 176
 177
 178     /* (non-Javadoc)
 179      * @see org.eclipse.ui.part.WorkbenchPart#setFocus()
 180      */
 181     @Override
 182     public void setFocus() {
 183         //alignmentArea.getToolkitComponent().redistributeHeight();
 184     }
 185 }